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Chadha Y, Khurana A, Schmoller KM. Eukaryotic cell size regulation and its implications for cellular function and dysfunction. Physiol Rev 2024; 104:1679-1717. [PMID: 38900644 DOI: 10.1152/physrev.00046.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 05/24/2024] [Accepted: 06/19/2024] [Indexed: 06/22/2024] Open
Abstract
Depending on cell type, environmental inputs, and disease, the cells in the human body can have widely different sizes. In recent years, it has become clear that cell size is a major regulator of cell function. However, we are only beginning to understand how the optimization of cell function determines a given cell's optimal size. Here, we review currently known size control strategies of eukaryotic cells and the intricate link of cell size to intracellular biomolecular scaling, organelle homeostasis, and cell cycle progression. We detail the cell size-dependent regulation of early development and the impact of cell size on cell differentiation. Given the importance of cell size for normal cellular physiology, cell size control must account for changing environmental conditions. We describe how cells sense environmental stimuli, such as nutrient availability, and accordingly adapt their size by regulating cell growth and cell cycle progression. Moreover, we discuss the correlation of pathological states with misregulation of cell size and how for a long time this was considered a downstream consequence of cellular dysfunction. We review newer studies that reveal a reversed causality, with misregulated cell size leading to pathophysiological phenotypes such as senescence and aging. In summary, we highlight the important roles of cell size in cellular function and dysfunction, which could have major implications for both diagnostics and treatment in the clinic.
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Affiliation(s)
- Yagya Chadha
- Institute of Functional Epigenetics, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Neuherberg, Germany
| | - Arohi Khurana
- Institute of Functional Epigenetics, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Neuherberg, Germany
| | - Kurt M Schmoller
- Institute of Functional Epigenetics, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Neuherberg, Germany
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2
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Liu X, Boelter G, Vollmer W, Banzhaf M, den Blaauwen T. Peptidoglycan Endopeptidase PBP7 Facilitates the Recruitment of FtsN to the Divisome and Promotes Peptidoglycan Synthesis in Escherichia coli. Mol Microbiol 2024. [PMID: 39344863 DOI: 10.1111/mmi.15321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 09/07/2024] [Accepted: 09/10/2024] [Indexed: 10/01/2024]
Abstract
Escherichia coli has many periplasmic hydrolases to degrade and modify peptidoglycan (PG). However, the redundancy of eight PG endopeptidases makes it challenging to define specific roles to individual enzymes. Therefore, the cellular role of PBP7 (encoded by pbpG) is not clearly defined. In this work, we show that PBP7 localizes in the lateral cell envelope and at midcell. The C-terminal α-helix of PBP7 is crucial for midcell localization but not for its activity, which is dispensable for this localization. Additionally, midcell localization of PBP7 relies on the assembly of FtsZ up to FtsN in the divisome, and on the activity of PBP3. PBP7 was found to affect the assembly timing of FtsZ and FtsN in the divisome. The absence of PBP7 slows down the assembly of FtsN at midcell. The ΔpbpG mutant exhibited a weaker incorporation of the fluorescent D-amino acid HADA, reporting on transpeptidase activity, compared to wild-type cells. This could indicate reduced PG synthesis at the septum of the ΔpbpG strain, explaining the slower accumulation of FtsN and suggesting that endopeptidase-mediated PG cleavage may be a rate-limiting step for septal PG synthesis.
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Affiliation(s)
- Xinwei Liu
- Bacterial Cell Biology and Physiology, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - Gabriela Boelter
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne, UK
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Manuel Banzhaf
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne, UK
| | - Tanneke den Blaauwen
- Bacterial Cell Biology and Physiology, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
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Hamm CW, Gray MJ. Inorganic polyphosphate and the stringent response coordinately control cell division and cell morphology in Escherichia coli. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.11.612536. [PMID: 39314361 PMCID: PMC11419118 DOI: 10.1101/2024.09.11.612536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Bacteria encounter numerous stressors in their constantly changing environments and have evolved many methods to deal with stressors quickly and effectively. One well known and broadly conserved stress response in bacteria is the stringent response, mediated by the alarmone (p)ppGpp. (p)ppGpp is produced in response to amino acid starvation and other nutrient limitations and stresses and regulates both the activity of proteins and expression of genes. Escherichia coli also makes inorganic polyphosphate (polyP), an ancient molecule evolutionary conserved across most bacteria and other cells, in response to a variety of stress conditions, including amino acid starvation. PolyP can act as an energy and phosphate storage pool, metal chelator, regulatory signal, and chaperone, among other functions. Here we report that E. coli lacking both (p)ppGpp and polyP have a complex phenotype indicating previously unknown overlapping roles for (p)ppGpp and polyP in regulating cell division, cell morphology, and metabolism. Disruption of either (p)ppGpp or polyP synthesis led to formation of filamentous cells, but simultaneous disruption of both pathways resulted in cells with heterogenous cell morphologies, including highly branched cells, severely mislocalized Z-rings, and cells containing substantial void spaces. These mutants also failed to grow when nutrients were limited, even when amino acids were added. These results provide new insights into the relationship between polyP synthesis and the stringent response in bacteria and point towards their having a joint role in controlling metabolism, cell division, and cell growth.
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Affiliation(s)
- Christopher W. Hamm
- Department of Microbiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Michael J. Gray
- Department of Microbiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
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4
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Xu X, Yang E, Chen Y. Progress in the Study of Optical Probes for the Detection of Formaldehyde. Crit Rev Anal Chem 2024; 54:1146-1172. [PMID: 35939357 DOI: 10.1080/10408347.2022.2107870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
Formaldehyde, one of the simplest reactive carbonyl substances, is involved in many physiological and pathological processes in living organisms. There is a large amount of data showing that abnormal elevation of formaldehyde is associated with a variety of diseases in the body, such as neurodegenerative diseases, Alzheimer's disease, cardiovascular diseases and cancer, and is also a representative carcinogen, so monitoring formaldehyde is of great importance for disease diagnosis and treatment. In this review, In this paper, we summarize and classify the last ten years of probes for the detection of formaldehyde according to different reaction mechanisms and discuss the structures and applications of the probes. Finally, we briefly describe the challenges and possible solutions in this field. We believe that more new probes provide powerful tools to study the function of formaldehyde in living systems.
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Affiliation(s)
- Xuexuan Xu
- The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Public Health Clinical Center, Hefei, China
| | - Erpei Yang
- The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Public Health Clinical Center, Hefei, China
| | - Yanyan Chen
- The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Public Health Clinical Center, Hefei, China
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5
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Mitchell SL, Kearns DB, Carlson EE. Penicillin-binding protein redundancy in Bacillus subtilis enables growth during alkaline shock. Appl Environ Microbiol 2024; 90:e0054823. [PMID: 38126750 PMCID: PMC10807460 DOI: 10.1128/aem.00548-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 11/13/2023] [Indexed: 12/23/2023] Open
Abstract
Penicillin-binding proteins (PBPs) play critical roles in cell wall construction, cell shape maintenance, and bacterial replication. Bacteria maintain a diversity of PBPs, indicating that despite their apparent functional redundancy, there is differentiation across the PBP family. Apparently-redundant proteins can be important for enabling an organism to cope with environmental stressors. In this study, we evaluated the consequence of environmental pH on PBP enzymatic activity in Bacillus subtilis. Our data show that a subset of PBPs in B. subtilis change activity levels during alkaline shock and that one PBP isoform is rapidly modified to generate a smaller protein (i.e., PBP1a to PBP1b). Our results indicate that a subset of the PBPs are favored for growth under alkaline conditions, while others are readily dispensable. Indeed, we found that this phenomenon could also be observed in Streptococcus pneumoniae, implying that it may be generalizable across additional bacterial species and further emphasizing the evolutionary benefit of maintaining many, seemingly-redundant periplasmic enzymes.IMPORTANCEMicrobes adapt to ever-changing environments and thrive over a vast range of conditions. While bacterial genomes are relatively small, significant portions encode for "redundant" functions. Apparent redundancy is especially pervasive in bacterial proteins that reside outside of the inner membrane. While conditions within the cytoplasm are carefully controlled, those of the periplasmic space are largely determined by the cell's exterior environment. As a result, proteins within this environmentally exposed region must be capable of functioning under a vast array of conditions, and/or there must be several similar proteins that have evolved to function under a variety of conditions. This study examines the activity of a class of enzymes that is essential in cell wall construction to determine if individual proteins might be adapted for activity under particular growth conditions. Our results indicate that a subset of these proteins are preferred for growth under alkaline conditions, while others are readily dispensable.
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Affiliation(s)
| | - Daniel B. Kearns
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Erin E. Carlson
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota, USA
- Departments of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, United States
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, United States
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Anderson SE, Vadia SE, McKelvy J, Levin PA. The transcription factor DksA exerts opposing effects on cell division depending on the presence of ppGpp. mBio 2023; 14:e0242523. [PMID: 37882534 PMCID: PMC10746185 DOI: 10.1128/mbio.02425-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE Cell division is a key step in the bacterial lifecycle that must be appropriately regulated to ensure survival. This work identifies the alarmone (p)ppGpp (ppGpp) as a general regulator of cell division, extending our understanding of the role of ppGpp beyond a signal for starvation and other stress. Even in nutrient-replete conditions, basal levels of ppGpp are essential for division to occur appropriately and for cell size to be maintained. This study establishes ppGpp as a "switch" that controls whether the transcription factor DksA behaves as a division activator or inhibitor. This unexpected finding enhances our understanding of the complex regulatory mechanisms employed by bacteria to coordinate division with diverse aspects of cell growth and stress response. Because division is an essential process, a better understanding of the mechanisms governing the assembly and activation of the division machinery could contribute to the development of novel therapeutics to treat bacterial infections.
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Affiliation(s)
- Sarah E. Anderson
- Department of Biology, Washington University in St. Louis, Saint Louis, Missouri, USA
| | - Stephen E. Vadia
- Department of Biology, Washington University in St. Louis, Saint Louis, Missouri, USA
| | - Jane McKelvy
- Department of Biology, Washington University in St. Louis, Saint Louis, Missouri, USA
| | - Petra Anne Levin
- Department of Biology, Washington University in St. Louis, Saint Louis, Missouri, USA
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7
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Xie LY, Xu YB, Ding XQ, Liang S, Li DL, Fu AK, Zhan XA. Itaconic acid and dimethyl itaconate exert antibacterial activity in carbon-enriched environments through the TCA cycle. Biomed Pharmacother 2023; 167:115487. [PMID: 37713987 DOI: 10.1016/j.biopha.2023.115487] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 09/17/2023] Open
Abstract
Itaconic acid (IA), a metabolite generated by the tricarboxylic acid (TCA) cycle in eukaryotic immune cells, and its derivative dimethyl itaconate (DI) exert antibacterial functions in intracellular environments. Previous studies suggested that IA and DI only inhibit bacterial growth in carbon-limited environments; however, whether IA and DI maintain antibacterial activity in carbon-enriched environments remains unknown. Here, IA and DI inhibited the bacteria with minimum inhibitory concentrations of 24.02 mM and 39.52 mM, respectively, in a carbon-enriched environment. The reduced bacterial pathogenicity was reflected in cell membrane integrity, motility, biofilm formation, AI-2/luxS, and virulence. Mechanistically, succinate dehydrogenase (SDH) activity and fumaric acid levels decreased in the IA and DI treatments, while isocitrate lyase (ICL) activity was upregulated. Inhibited TCA circulation was also observed through untargeted metabolomics. In addition, energy-related aspartate metabolism and lysine degradation were suppressed. In summary, these results indicated that IA and DI reduced bacterial pathogenicity while exerting antibacterial functions by inhibiting TCA circulation. This study enriches knowledge on the inhibition of bacteria by IA and DI in a carbon-mixed environment, suggesting an alternative method for treating bacterial infections by immune metabolites.
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Affiliation(s)
- L Y Xie
- Key Laboratory of Animal Nutrition and Feed in East China, Ministry of Agriculture and Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Feed Science Institute, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - Y B Xu
- Key Laboratory of Animal Nutrition and Feed in East China, Ministry of Agriculture and Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Feed Science Institute, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - X Q Ding
- Key Laboratory of Animal Nutrition and Feed in East China, Ministry of Agriculture and Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Feed Science Institute, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - S Liang
- Key Laboratory of Animal Nutrition and Feed in East China, Ministry of Agriculture and Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Feed Science Institute, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - D L Li
- Key Laboratory of Animal Nutrition and Feed in East China, Ministry of Agriculture and Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Feed Science Institute, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - A K Fu
- Key Laboratory of Animal Nutrition and Feed in East China, Ministry of Agriculture and Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Feed Science Institute, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - X A Zhan
- Key Laboratory of Animal Nutrition and Feed in East China, Ministry of Agriculture and Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Feed Science Institute, College of Animal Science, Zhejiang University, Hangzhou 310058, China.
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8
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Anderson SE, Vadia SE, McKelvy J, Levin PA. The transcription factor DksA exerts opposing effects on cell division depending on the presence of ppGpp. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.15.540843. [PMID: 37293059 PMCID: PMC10245573 DOI: 10.1101/2023.05.15.540843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Bacterial cell size is a multifactorial trait that is influenced by variables including nutritional availability and the timing of cell division. Prior work revealed a negative correlation between the alarmone (p)ppGpp (ppGpp) and cell length in Escherichia coli , suggesting that ppGpp may promote assembly of the division machinery (divisome) and cytokinesis in this organism. To clarify this counterintuitive connection between a starvation induced stress response effector and cell proliferation, we undertook a systematic analysis of growth and division in E. coli cells defective in ppGpp synthesis and/or engineered to overproduce the alarmone. Our data indicate that ppGpp acts indirectly on divisome assembly through its role as a global mediator of transcription. Loss of either ppGpp (ppGpp 0 ) or the ppGpp-associated transcription factor DksA led to increased average length, with ppGpp 0 mutants also exhibiting a high frequency of extremely long filamentous cells. Using heat-sensitive division mutants and fluorescently labeled division proteins, we confirmed that ppGpp and DksA are cell division activators. We found that ppGpp and DksA regulate division through their effects on transcription, although the lack of known division genes or regulators in available transcriptomics data strongly suggests that this regulation is indirect. Surprisingly, we also found that DksA inhibits division in ppGpp 0 cells, contrary to its role in a wild-type background. We propose that the ability of ppGpp to switch DksA from a division inhibitor to a division activator helps tune cell length across different concentrations of ppGpp. Importance Cell division is a key step in the bacterial lifecycle that must be appropriately regulated to ensure survival. This work identifies the alarmone ppGpp as a general regulator of cell division, extending our understanding of the role of ppGpp beyond a signal for starvation and other stress. Even in nutrient replete conditions, basal levels of ppGpp are essential for division to occur appropriately and for cell size to be maintained. This study establishes ppGpp as a "switch" that controls whether the transcription factor DksA behaves as a division activator or inhibitor. This unexpected finding enhances our understanding of the complex regulatory mechanisms employed by bacteria to coordinate division with diverse aspects of cell growth and stress response. Because division is an essential process, a better understanding the mechanisms governing assembly and activation of the division machinery could contribute to the development of novel therapeutics to treat bacterial infections.
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9
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Mitchell SL, Kearns DB, Carlson EE. Penicillin-binding protein redundancy in Bacillus subtilis enables growth during alkaline shock. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.20.533529. [PMID: 36993441 PMCID: PMC10055284 DOI: 10.1101/2023.03.20.533529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Penicillin-binding proteins (PBPs) play critical roles in cell wall construction, cell shape, and bacterial replication. Bacteria maintain a diversity of PBPs, indicating that despite their apparent functional redundancy, there is differentiation across the PBP family. Seemingly redundant proteins can be important for enabling an organism to cope with environmental stressors. We sought to evaluate the consequence of environmental pH on PBP enzymatic activity in Bacillus subtilis. Our data show that a subset of B. subtilis PBPs change activity levels during alkaline shock and that one PBP isoform is rapidly modified to generate a smaller protein (i.e., PBP1a to PBP1b). Our results indicate that a subset of the PBPs are preferred for growth under alkaline conditions, while others are readily dispensable. Indeed, we found that this phenomenon could also be observed in Streptococcus pneumoniae, implying that it may be generalizable across additional bacterial species and further emphasizing the evolutionary benefit of maintaining many, seemingly redundant periplasmic enzymes.
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Affiliation(s)
| | - Daniel B. Kearns
- Department of Biology, Indiana University, Bloomington, Indiana 47405
| | - Erin E. Carlson
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
- Departments of Medicinal Chemistry, Biochemistry, Molecular Biology and Biophysics, and Pharmacology, University of Minnesota, Minneapolis, Minnesota 55455
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10
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Shimasawa M, Sakamaki JI, Maeda T, Mizushima N. The pH-sensing Rim101 pathway regulates cell size in budding yeast. J Biol Chem 2023; 299:102973. [PMID: 36738789 PMCID: PMC10011510 DOI: 10.1016/j.jbc.2023.102973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 01/28/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Although cell size regulation is crucial for cellular functions in a variety of organisms from bacteria to humans, the underlying mechanisms remain elusive. Here, we identify Rim21, a component of the pH-sensing Rim101 pathway, as a positive regulator of cell size through a flow cytometry-based genome-wide screen of Saccharomyces cerevisiae deletion mutants. We found that mutants defective in the Rim101 pathway were consistently smaller than wildtype cells in the log and stationary phases. We show that the expression of the active form of Rim101 increased the size of wildtype cells. Furthermore, the size of wildtype cells increased in response to external alkalization. Microscopic observation revealed that this cell size increase was associated with changes in both vacuolar and cytoplasmic volume. We also found that these volume changes were dependent on Rim21 and Rim101. In addition, a mutant lacking Vph1, a component of V-ATPase that is transcriptionally regulated by Rim101, was also smaller than wildtype cells, with no increase in size in response to alkalization. We demonstrate that the loss of Vph1 suppressed the Rim101-induced increase in cell size under physiological pH conditions. Taken together, our results suggest that the cell size of budding yeast is regulated by the Rim101-V-ATPase axis under physiological conditions as well as in response to alkaline stresses.
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Affiliation(s)
- Masaru Shimasawa
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jun-Ichi Sakamaki
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tatsuya Maeda
- Department of Biology, Hamamatsu University School of Medicine, Shizuoka, Japan
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, Japan.
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11
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Yahashiri A, Kaus GM, Popham DL, Houtman JCD, Weiss DS. Comparative Study of Bacterial SPOR Domains Identifies Functionally Important Differences in Glycan Binding Affinity. J Bacteriol 2022; 204:e0025222. [PMID: 36005810 PMCID: PMC9487507 DOI: 10.1128/jb.00252-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/05/2022] [Indexed: 11/20/2022] Open
Abstract
Bacterial SPOR domains target proteins to the divisome by binding septal peptidoglycan (PG) at sites where cell wall amidases have removed stem peptides. These PG structures are referred to as denuded glycans. Although all characterized SPOR domains bind denuded glycans, whether there are differences in affinity is not known. Here, we use isothermal titration calorimetry (ITC) to determine the relative PG glycan binding affinity (<i>K</i><sub>d</sub>) of four Escherichia coli SPOR domains and one Cytophaga hutchinsonii SPOR domain. We found that the <i>K</i><sub>d</sub> values ranged from approximately 1 μM for E. coli DamX<sup>SPOR</sup> and <i>C. hutchinsonii</i> CHU2221<sup>SPOR</sup> to about 10 μM for E. coli FtsN<sup>SPOR</sup>. To investigate whether these differences in PG binding affinity are important for SPOR domain protein function, we constructed and characterized a set of DamX and FtsN "swap" proteins. As expected, all SPOR domain swap proteins localized to the division site, and, in the case of FtsN, all of the heterologous SPOR domains supported cell division. However, for DamX, only the high-affinity SPOR domain from CHU2221 supported normal function in cell division. In summary, different SPOR domains bind denuded PG glycans with different affinities, which appears to be important for the functions of some SPOR domain proteins (e.g., DamX) but not for the functions of others (e.g., FtsN). <b>IMPORTANCE</b> SPOR domain proteins are prominent components of the cell division apparatus in a wide variety of bacteria. The primary function of SPOR domains is targeting proteins to the division site, which they accomplish by binding to septal peptidoglycan. However, whether SPOR domains have any functions beyond septal targeting is unknown. Here, we show that SPOR domains vary in their PG binding affinities and that, at least in the case of the E. coli cell division protein DamX, having a high-affinity SPOR domain contributes to proper function.
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Affiliation(s)
- Atsushi Yahashiri
- Department of Microbiology and Immunology, Carver College of Medicine, The University of Iowa, Iowa City, Iowa, USA
| | - Gabriela M. Kaus
- Department of Microbiology and Immunology, Carver College of Medicine, The University of Iowa, Iowa City, Iowa, USA
| | - David L. Popham
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Jon C. D. Houtman
- Department of Microbiology and Immunology, Carver College of Medicine, The University of Iowa, Iowa City, Iowa, USA
| | - David S. Weiss
- Department of Microbiology and Immunology, Carver College of Medicine, The University of Iowa, Iowa City, Iowa, USA
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12
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Levin PA, Janakiraman A. Localization, Assembly, and Activation of the Escherichia coli Cell Division Machinery. EcoSal Plus 2021; 9:eESP00222021. [PMID: 34910577 PMCID: PMC8919703 DOI: 10.1128/ecosalplus.esp-0022-2021] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 11/14/2021] [Indexed: 01/01/2023]
Abstract
Decades of research, much of it in Escherichia coli, have yielded a wealth of insight into bacterial cell division. Here, we provide an overview of the E. coli division machinery with an emphasis on recent findings. We begin with a short historical perspective into the discovery of FtsZ, the tubulin homolog that is essential for division in bacteria and archaea. We then discuss assembly of the divisome, an FtsZ-dependent multiprotein platform, at the midcell septal site. Not simply a scaffold, the dynamic properties of polymeric FtsZ ensure the efficient and uniform synthesis of septal peptidoglycan. Next, we describe the remodeling of the cell wall, invagination of the cell envelope, and disassembly of the division apparatus culminating in scission of the mother cell into two daughter cells. We conclude this review by highlighting some of the open questions in the cell division field, emphasizing that much remains to be discovered, even in an organism as extensively studied as E. coli.
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Affiliation(s)
- Petra Anne Levin
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
- Center for Science & Engineering of Living Systems (CSELS), McKelvey School of Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Anuradha Janakiraman
- Department of Biology, The City College of New York, New York, New York, USA
- Programs in Biology and Biochemistry, The Graduate Center of the City University of New York, New York, New York, USA
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13
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Yang M, Yin Y, Wang F, Bao X, Long L, Tan B, Yin Y, Chen J. Effects of dietary rosemary extract supplementation on growth performance, nutrient digestibility, antioxidant capacity, intestinal morphology, and microbiota of weaning pigs. J Anim Sci 2021; 99:6346706. [PMID: 34370023 DOI: 10.1093/jas/skab237] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/06/2021] [Indexed: 12/20/2022] Open
Abstract
Rosemary (Rosmarinus officinalis L.) extract (RE) has multiple pharmacological and biological activities, including the use as a food additive and medicine. This study was conducted to investigate the effects of dietary RE supplementation on the growth performance, nutrient digestibility, antioxidant capacity, intestinal morphology, and microbiota of weaning piglets. A total of 192 crossbred weaned piglets [Duroc × (Large White × Landrace)] (initial body weight = 6.65 ± 0.33 kg, weaned days = 23 ± 1 d) were group housed (six pigs per pen; n = 8 pens/treatment). Pigs were fed a corn-soybean meal-based control diet or the basal diet supplemented with 100, 200, or 400 mg/kg RE. Pigs were allowed ad libitum access to fed for 21 d. The growth performance and apparent total tract digestibility of nutrients, and intestinal morphology and antioxidant status were evaluated. The components of the microbial microflora were also determined in the cecal samples. Compared with the control, dietary supplementation with RE increased the final body weight, average daily gain, and average daily feed intake (linear, P = 0.038, 0.016, and 0.009, respectively), and decreased the diarrhea ratio in piglets (linear, P < 0.05). The digestibility of crude protein (linear, P = 0.034) and gross energy (linear, P = 0.046) increased with treatment with RE. Piglets fed RE showed longer villus height (linear, P = 0.037 and 0.028, respectively) and villus height/crypt depth (linear, P = 0.004 and 0.012; quadratic, P = 0.023 and 0.036, respectively) in the jejunum and ileum, in addition to a lesser crypt depth in the jejunum (linear, P = 0.019) and ileum (quadratic, P = 0.042). The addition of RE increased the activity of superoxide dismutase (linear, P = 0.035 and 0.008, respectively) and glutathione peroxidase activity (linear, P = 0.027 and 0.039, respectively) and decreased the content of malondialdehyde (linear, P = 0.041 and 0.013; quadratic, P = 0.023 and 0.005, respectively) in the serum and liver. Dietary RE supplementation, compared with the control, increased the number of Bifidobacterium (linear, P = 0.034) and Bacteroidetes (linear, P = 0.029), while decreased Escherichia coli (linear, P = 0.008; quadratic, P = 0.014) in the cecal contents. Thus, dietary RE supplementation can improve growth performance, nutrient digestibility, antioxidant capacity, intestinal morphology, and the microbiota in weaned piglets, and 200 mg/kg may be considered the optimum dosage.
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Affiliation(s)
- Mei Yang
- Animal Nutritional Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan 410128, PR China
| | - Yexin Yin
- Animal Nutritional Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan 410128, PR China
| | - Fang Wang
- Animal Nutritional Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan 410128, PR China
| | - Xuetai Bao
- CAS Key Laboratory of Agro ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Changsha 410125, PR China
| | - Lina Long
- School of Life Science and Engineering, Foshan University, Foshan 528231, China
| | - Bie Tan
- Animal Nutritional Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan 410128, PR China
| | - Yulong Yin
- Animal Nutritional Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan 410128, PR China.,CAS Key Laboratory of Agro ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Changsha 410125, PR China
| | - Jiashun Chen
- Animal Nutritional Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan 410128, PR China.,CAS Key Laboratory of Agro ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Changsha 410125, PR China
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14
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Mueller EA, Iken AG, Ali Öztürk M, Winkle M, Schmitz M, Vollmer W, Di Ventura B, Levin PA. The active repertoire of Escherichia coli peptidoglycan amidases varies with physiochemical environment. Mol Microbiol 2021; 116:311-328. [PMID: 33666292 DOI: 10.1111/mmi.14711] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/27/2021] [Accepted: 03/02/2021] [Indexed: 12/17/2022]
Abstract
Nearly all bacteria are encased in peptidoglycan, an extracytoplasmic matrix of polysaccharide strands crosslinked through short peptide stems. In the Gram-negative model organism Escherichia coli, more than 40 synthases and autolysins coordinate the growth and division of the peptidoglycan sacculus in the periplasm. The precise contribution of many of these enzymes to peptidoglycan metabolism remains unclear due to significant apparent redundancy, particularly among the autolysins. E. coli produces three major LytC-type-N-acetylmuramoyl-L-alanine amidases, which share a role in separating the newly formed daughter cells during cytokinesis. Here, we reveal two of the three amidases that exhibit growth medium-dependent changes in activity. Specifically, we report acidic growth conditions stimulate AmiB-and to a lesser extent, AmiC-amidase activity. Combining genetic, biochemical, and computational analyses, we demonstrate that low pH-dependent stimulation of AmiB is mediated through the periplasmic amidase activators NlpD, EnvC, and ActS (formerly known as YgeR). Although NlpD and EnvC promote amidase activity across pH environments, ActS preferentially stimulates AmiB activity in acidic conditions. Altogether, our findings support partially overlapping roles for E. coli amidases and their regulators in cell separation and illuminate the physiochemical environment as an important mediator of cell wall enzyme activity.
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Affiliation(s)
- Elizabeth A Mueller
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA.,Center for Science & Engineering of Living Systems (CSELS), McKelvey School of Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Abbygail G Iken
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - Mehmet Ali Öztürk
- Signalling Research Centers BIOSS and CIBSS, McKelvey School of Engineering, University of Freiburg, Freiburg, Germany.,Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Matthias Winkle
- The Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Mirko Schmitz
- Signalling Research Centers BIOSS and CIBSS, McKelvey School of Engineering, University of Freiburg, Freiburg, Germany.,Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Waldemar Vollmer
- The Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Barbara Di Ventura
- Signalling Research Centers BIOSS and CIBSS, McKelvey School of Engineering, University of Freiburg, Freiburg, Germany.,Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Petra Anne Levin
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA.,Center for Science & Engineering of Living Systems (CSELS), McKelvey School of Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
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15
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When the metabolism meets the cell cycle in bacteria. Curr Opin Microbiol 2021; 60:104-113. [PMID: 33677348 DOI: 10.1016/j.mib.2021.02.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 12/20/2022]
Abstract
Nutrients availability is the sinews of the war for single microbial cells, driving growth and cell cycle progression. Therefore, coordinating cellular processes with nutrients availability is crucial, not only to survive upon famine or fluctuating conditions but also to rapidly thrive and colonize plentiful environments. While metabolism is traditionally seen as a set of chemical reactions taking place in cells to extract energy and produce building blocks from available nutrients, numerous connections between metabolic pathways and cell cycle phases have been documented. The few regulatory systems described at the molecular levels show that regulation is mediated either by a second messenger molecule or by a metabolite and/or a metabolic enzyme. In the latter case, a secondary moonlighting regulatory function evolved independently of the primary catalytic function of the enzyme. In this review, we summarize our current understanding of the complex cross-talks between metabolism and cell cycle in bacteria.
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16
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Influence of Lactic Acid on Cell Cycle Progressions in Lactobacillus bulgaricus During Batch Culture. Appl Biochem Biotechnol 2020; 193:912-924. [PMID: 33206317 DOI: 10.1007/s12010-020-03459-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 11/08/2020] [Indexed: 02/02/2023]
Abstract
Lactic acid has been proved to inhibit the proliferation of lactic acid bacteria in the fermentation process. To shed light on the cell cycle alterations in acidic conditions, the cell division of Lactobacillus bulgaricus sp1.1 in batch culture was analyzed directly by implementing of the intracellular fluorescent tracking assay in different pH adjusted by lactic acid. Cell proliferation and cell division were investigated to be negatively controlled by the decrease of pH, and pH 4.1 was the critical condition of downregulating cell division but retains cell culturability. The cell area and cell length in pH 4.1 were examined by using fluorescent labeling, and they reduced to about 29.18-34.89% and 32.67-40% of cells cultured in the unacidified medium, respectively. The DNA replication initiation was undergoing prompted by the low extent of DNA condensation and higher expression of the dnaA gene in this critical pH. The results indicated that the cell cycle progressions of Lactobacillus bulgaricus sp1.1 in acidic conditions were arrested at intracellular biomass accumulation and cell division stage. These findings provide fundamental insight into cell cycle control of the acidic environment in Lactobacillus bulgaricus sp1.1.
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17
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Abstract
Single-celled organisms must adapt their physiology to persist and propagate across a wide range of environmental conditions. The growth and division of bacterial cells depend on continuous synthesis of an essential extracellular barrier: the peptidoglycan cell wall, a polysaccharide matrix that counteracts turgor pressure and confers cell shape. Unlike many other essential processes and structures within the bacterial cell, the peptidoglycan cell wall and its synthesis machinery reside at the cell surface and are thus uniquely vulnerable to the physicochemical environment and exogenous threats. In addition to the diversity of stressors endangering cell wall integrity, defects in peptidoglycan metabolism require rapid repair in order to prevent osmotic lysis, which can occur within minutes. Here, we review recent work that illuminates mechanisms that ensure robust peptidoglycan metabolism in response to persistent and acute environmental stress. Advances in our understanding of bacterial cell wall quality control promise to inform the development and use of antimicrobial agents that target the synthesis and remodeling of this essential macromolecule.IMPORTANCE Nearly all bacteria are encased in a peptidoglycan cell wall, an essential polysaccharide structure that protects the cell from osmotic rupture and reinforces cell shape. The integrity of this protective barrier must be maintained across the diversity of environmental conditions wherein bacteria replicate. However, at the cell surface, the cell wall and its synthesis machinery face unique challenges that threaten their integrity. Directly exposed to the extracellular environment, the peptidoglycan synthesis machinery encounters dynamic and extreme physicochemical conditions, which may impair enzymatic activity and critical protein-protein interactions. Biotic and abiotic stressors-including host defenses, cell wall active antibiotics, and predatory bacteria and phage-also jeopardize peptidoglycan integrity by introducing lesions, which must be rapidly repaired to prevent cell lysis. Here, we review recently discovered mechanisms that promote robust peptidoglycan synthesis during environmental and acute stress and highlight the opportunities and challenges for the development of cell wall active therapeutics.
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